[Bioperl-l] Re: Target class on gbrowse

[Lincoln Stein]

Hi Marco,

I've just modified the way that Bio::DB::GFF handles the GFF group field in 
order to be compliant with the way that Bioperl's GFF formatter does it.  On 
reading the Sanger spec, I've come to the conclusion that the files that 
Sanger produces in its Acedb dumps don't exactly match the specification!

To get this mod, you need to update to the current CVS version of bioperl.

Best,

Lincoln


On Monday 09 September 2002 05:05 pm, Marco Aurelio Valtas Cunha wrote:
> Hi Lincoln,
>
> When I'm using SeqFeature::Generic to get a GFF format, I use this
> syntax to have a Target ( blast ):
>
> ...code...
>
>   -tag     => {
>      Target => "Sequence:$query ".$start." ".$end,
>               }
>
> ...code...
>
> but this cause the start and end to be inside the quotes, like:
>
> Target "Sequence:PM2-MT0009-180400-001-g02 9 374"
>
> This can cause problems with gbrowse?. since in your documentation the
> examples has the numbers outside the quotes. Of course I'm having not
> track displayed, so I'm hunting bugs, check this GFF, it can cause trouble?
>
> <GFF>
> Chr13   ORESTES.MEGABLAST       alignment       71191038        71191231
>         5e-58   +       .       Target
> "Sequence:PM2-MT0009-180400-001-h01 6 40"
> </GFF>
>
> Thank you.
> Marco.

-- 
Lincoln Stein
lstein@cshl.org